Can I use a vertex shader and Cycles at the same time?
Cycles uses a very different rendering system and is independent of openGL, so features are going to be different and you won't be able to combine these shaders. There is an experimental real displacement feature that might help, but I think you would be better trying python if you have some idea what the code should look like. 

You could use an application handler on the frame_change_pre event to create this effect.
(https://www.blender.org/api/blender_python_api_2_77_1/bpy.app.handlers.html?highlight=handler)

If the changes are fairly simple, a bunch of shapekeys for various parts of the mesh may be easier, and just key/animate them manually.